ci: improve update pins job (#1344)

* ci: improve update pins job

* fix pre-commit

* Restore workflow_dispatch

.github/workflows/update-pinned-env.yml

@@ -4,15 +4,15 @@ on:
   push:
     paths:
     - envs/environment.yaml
-  # Run every Sunday at 5:00 UTC
   schedule:
-  - cron: "0 5 * * 0"
+  - cron: "0 8 1,16 * *" # Bi-weekly
   workflow_dispatch:
 
+env:
+  BASE_ENV: envs/environment.yaml
 
 jobs:
   update-pinned-environment:
-    # the update is always needed for env changes in main and sometimes for other branches
     if: ${{ github.ref == 'refs/heads/main' || github.event_name == 'workflow_dispatch' }}
     name: Update pinned envs
     runs-on: ${{ matrix.os }}-latest
@@ -35,11 +35,12 @@ jobs:
       uses: conda-incubator/setup-miniconda@v3
       with:
         activate-environment: ${{ github.event.repository.name }}
-        environment-file: envs/environment.yaml
+        channels: bioconda,conda-forge,defaults
+        environment-file: ${{ env.BASE_ENV }}
 
     - name: Update pinned environment per OS
       run: |
-        conda env export --name ${{ github.event.repository.name }} --no-builds > envs/${{ matrix.suffix }}-pinned.yaml
+        conda env export --name ${{ github.event.repository.name }} --no-builds -c conda-forge -c bioconda --override-channels > envs/${{ matrix.suffix }}-pinned.yaml
 
     - name: Add SPDX header
       if: ${{ matrix.suffix != 'windows' }}

.pre-commit-config.yaml

@@ -73,6 +73,7 @@ repos:
   rev: v2.14.0
   hooks:
   - id: pretty-format-yaml
+    exclude: pinned\.yaml$
     args: [--autofix, --indent, '2', --preserve-quotes]
 
 # Use yamllint to check for valid YAML files and list syntax errors